Compute.GeneTree_Likelihoods: Compute.GeneTree_Likelihoods: function to compute gene tree...

In radamsRHA/SpeciesTopoTestR: Likelihood-based tests of species topologies in R

Compute.GeneTree_Likelihoods: function to compute gene tree likelihoods using STELL

Description

This function returns a vector of gene tree likelihoods given a set of gene trees and a particular species tree

Usage

Compute.GeneTree_Likelihoods(
  handle.SpeciesTree,
  handle.GeneTrees,
  string.PathDir
)

Arguments

handle.SpeciesTree	Phylo object of the species tree
handle.GeneTrees	Phylo object of gene trees
string.PathDir	String of the path to a parent directory used for simulating gene trees

Value

vector.GeneTreeProbs Vector of gene tree likelihoods for each gene tree provided

Examples

################
# Load depends #
################
library(SpeciesTopoTestR)
library(ape)

#################################
# Generate example species trees #
#################################
handle.SpeciesTree1 <- read.tree(text = "(A:1.0,(B:0.5,(C:1.0,D:1.0):1.5):0.5);")

#################################################
# Simlate a set of gene trees for species tree1 #
#################################################
handle.Simulated_GeneTrees <- Simulate.GeneTrees_From_SpeciesTree3(handle.SpeciesTree = handle.SpeciesTree1,
                                                                  string.PathDir = '~/Desktop/',
                                                                  numeric.NumberOfGeneTrees = 100)


vector.GeneTree_Likelihoods <- Compute.GeneTree_Likelihoods(handle.SpeciesTree = handle.SpeciesTree1,
                                                            handle.GeneTrees = handle.Simulated_GeneTrees,
                                                            string.PathDir = '~/Desktop/')

radamsRHA/SpeciesTopoTestR documentation built on Sept. 5, 2022, 7:37 p.m.